Question: Convert Fdr Control Q-Value To P-Value
gravatar for J.F.Jiang
8.1 years ago by
J.F.Jiang850 wrote:

Hi everyone,

I have downloaded a set of processed data of gene expression relationship, while they offered a result of q value. Since I want to use the p value to adjust the next step, how can I convert this Q value to p value?


ADD COMMENTlink modified 7.8 years ago by admiral.david0 • written 8.1 years ago by J.F.Jiang850

Is it possible that your dataset was analyzed by a method that does not produce p-values? For example, baySeq, a tool for testing differential expression in RNA-Seq data, produces posterior probabilities from a Bayesian analysis and calculates FDR directly from them. The nature of the calculations is such that no p-value is involved.

ADD REPLYlink written 8.1 years ago by Ryan Thompson3.4k

How did you get your Q values ?

ADD REPLYlink written 8.1 years ago by
gravatar for David Quigley
8.1 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

I think the short answer is that you can't. One way to calculate a Q value estimate is from a distribution of P values (e.g. the way Storey's qvalue works), but I don't think there is any way to reconstruct the P value distribution from a set of estimated Q values. You should calculating the P values directly if that's what you want. The manual to the qvalue package has more information about what a Q value is and how it can be calculated, which you might want to read.

ADD COMMENTlink written 8.1 years ago by David Quigley11k

YES, I have read the wiki of Q value and methods of original author, I can not convert this Q, but I can still estimate the p-value

ADD REPLYlink written 8.1 years ago by J.F.Jiang850
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